MyProteinNet: Build up-to-date protein interaction networks for organisms, tissues and user-defined contexts

Nucleic Acids Research

Volumn 43, Issue W1, 2015, Pages W258-W263

  Basha, Omer ^a   Flom, Dvir ^a   Barshir, Ruth ^a   Smoly, Ilan ^a   Tirman, Shoval ^a   Yeger Lotem, Esti ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; GENE ONTOLOGY; HUMAN; MOLECULAR GENETICS; MYPROTEINNET; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; WEB BROWSER; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; INTERNET; PROCEDURES; PROTEIN DATABASE;

DATABASES, PROTEIN; GENE EXPRESSION PROFILING; GENE ONTOLOGY; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; PROTEIN INTERACTION MAPPING; SOFTWARE;

EID: 84979866839     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv515     Document Type: Article

References (50)

1. Breitkreutz, A., Choi, H., Sharom, J.R., Boucher, L., Neduva, V., Larsen, B., Lin, Z.Y., Breitkreutz, B.J., Stark, C., Liu, G. et al. (2010) A global protein kinase and phosphatase interaction network in yeast. Science, 328, 1043-1046.
2. Taipale, M., Tucker, G., Peng, J., Krykbaeva, I., Lin, Z.Y., Larsen, B., Choi, H., Berger, B., Gingras, A.C. and Lindquist, S. (2014) A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. Cell, 158, 434-448.
3. Yu, H., Braun, P., Yildirim, M.A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N. et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science, 322, 104-110.
4. Arabidopsis Interactome Mapping Consortium. (2011) Evidence for network evolution in an Arabidopsis interactome map. Science, 333, 601-607.
5. Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C.E., Godwin, B., Vitols, E. et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
6. Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N. et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-1178.
7. Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F.H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S. et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122, 957-968.
8. Rolland, T., Tasan, M., Charloteaux, B., Pevzner, S.J., Zhong, Q., Sahni, N., Yi, S., Lemmens, I., Fontanillo, C., Mosca, R. et al. (2014) A proteome-scale map of the human interactome network. Cell, 159, 1212-1226.
9. Vidal, M., Cusick, M.E. and Barabasi, A.L. (2011) Interactome networks and human disease. Cell, 144, 986-998.
10. De Las Rivas, J. and Fontanillo, C. (2010) Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput. Biol., 6, e1000807.
11. Pujana, M.A., Han, J.D., Starita, L.M., Stevens, K.N., Tewari, M., Ahn, J.S., Rennert, G., Moreno, V., Kirchhoff, T., Gold, B. et al. (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat. Genet., 39, 1338-1349.
12. Paz, A., Brownstein, Z., Ber, Y., Bialik, S., David, E., Sagir, D., Ulitsky, I., Elkon, R., Kimchi, A., Avraham, K.B. et al. (2011) SPIKE: a database of highly curated human signaling pathways. Nucleic Acids Res., 39, D793-D799.
13. Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
14. Breitkreutz, B.J., Stark, C., Reguly, T., Boucher, L., Breitkreutz, A., Livstone, M., Oughtred, R., Lackner, D.H., Bahler, J., Wood, V. et al. (2008) The BioGRID Interaction Database: 2008 update. Nucleic Acids Res., 36, D637-D640.
15. Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U. and Eisenberg, D. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
16. Bruckner, A., Polge, C., Lentze, N., Auerbach, D. and Schlattner, U. (2009) Yeast two-hybrid, a powerful tool for systems biology. Int. J. Mol. Sci., 10, 2763-2788.
17. Uetz, P. and Finley, R.L. (2005) From protein networks to biological systems. FEBS Lett., 579, 1821-1827.
18. Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J. and Bork, P. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res., 39, D561-D568.
19. Aranda, B., Blankenburg, H., Kerrien, S., Brinkman, F.S., Ceol, A., Chautard, E., Dana, J.M., De Las Rivas, J., Dumousseau, M., Galeota, E. et al. (2011) PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat. Methods, 8, 528-529.
20. Prieto, C. and De Las Rivas, J. (2006) APID: Agile Protein Interaction Data Analyzer. Nucleic Acids Res., 34, W298-W302.
21. Myers, C.L., Robson, D., Wible, A., Hibbs, M.A., Chiriac, C., Theesfeld, C.L., Dolinski, K. and Troyanskaya, O.G. (2005) Discovery of biological networks from diverse functional genomic data. Genome Biol., 6, R114.
22. Yeger-Lotem, E., Riva, L., Su, L.J., Gitler, A.D., Cashikar, A.G., King, O.D., Auluck, P.K., Geddie, M.L., Valastyan, J.S., Karger, D.R. et al. (2009) Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat. Genet., 41, 316-323.
23. Guan, Y., Gorenshteyn, D., Burmeister, M., Wong, A.K., Schimenti, J.C., Handel, M.A., Bult, C.J., Hibbs, M.A. and Troyanskaya, O.G. (2012) Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput. Biol., 8, e1002694.
24. Magger, O., Waldman, Y.Y., Ruppin, E. and Sharan, R. (2012) Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PLoS Comput. Biol., 8, e1002690.
25. Luscombe, N.M., Babu, M.M., Yu, H., Snyder, M., Teichmann, S.A. and Gerstein, M. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431, 308-312.
26. de Lichtenberg, U., Jensen, L.J., Brunak, S. and Bork, P. (2005) Dynamic complex formation during the yeast cell cycle. Science, 307, 724-727.
27. Bossi, A. and Lehner, B. (2009) Tissue specificity and the human protein interaction network. Mol. Syst. Biol., 5, 260.
28. Vinayagam, A., Hu, Y., Kulkarni, M., Roesel, C., Sopko, R., Mohr, S.E. and Perrimon, N. (2013) Protein complex-based analysis framework for high-throughput data sets. Sci. Signal., 6, 264.
29. Guan, Y., Gorenshteyn, D., Burmeister, M., Wong, A.K., Schimenti, J.C., Handel, M.A., Bult, C.J., Hibbs, M.A. and Troyanskaya, O.G. (2012) Tissue-specific functional networks for prioritizing phenotype and disease genes. Comput. Biol., 8, e1002694.
30. Schaefer, M.H., Fontaine, J.-F., Vinayagam, A., Porras, P., Wanker, E.E. and Andrade-Navarro, M.A. (2012) HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One, 7, e31826.
31. Kamburov, A., Stelzl, U. and Herwig, R. (2012) IntScore: a web tool for confidence scoring of biological interactions. Nucleic Acids Res., 40, W140-W146.
32. Barshir, R., Basha, O., Eluk, A., Smoly, I.Y., Lan, A. and Yeger-Lotem, E. (2013) The TissueNet database of human tissue protein-protein interactions. Nucleic Acids Res., 41, D841-D844.
33. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
34. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
35. Basha, O., Tirman, S., Eluk, A. and Yeger-Lotem, E. (2013) ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes-now with human data. Nucleic Acids Res., 41, W198-W203.
36. Cunningham, F., Amode, M.R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G. and Fitzgerald, S. (2015) Ensembl 2015. Nucleic Acids Res., 43, D662-D669.
37. Wu, C., MacLeod, I. and Su, A.I. (2013) BioGPS and MyGene.info: organizing online, gene-centric information. Nucleic Acids Res., 41, D561-D565.
38. Hishiki, T., Kawamoto, S., Morishita, S. and Okubo, K. (2000) BodyMap: a human and mouse gene expression database. Nucleic Acids Res., 28, 136-138.
39. Ramsköld, D., Wang, E.T., Burge, C.B. and Sandberg, R. (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol., 5, e1000598.
40. Berglund, L., Bj örling, E., Oksvold, P., Fagerberg, L., Asplund, A., Szigyarto, C.A.-K., Persson, A., Ottosson, J., Wernérus, H. and Nilsson, P. (2008) A genecentric Human Protein Atlas for expression profiles based on antibodies. Mol. Cell. Proteomics, 7, 2019-2027.
41. Barshir, R., Shwartz, O., Smoly, I.Y. and Yeger-Lotem, E. (2014) Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PLoS Comput. Biol., 10, e1003632.
42. Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W. and Selbach, M. (2011) Global quantification of mammalian gene expression control. Nature, 473, 337-342.
43. Berglund, L., Bjorling, E., Oksvold, P., Fagerberg, L., Asplund, A., Szigyarto, C.A., Persson, A., Ottosson, J., Wernerus, H., Nilsson, P. et al. (2008) A genecentric Human Protein Atlas for expression profiles based on antibodies. Mole. Cell. Proteomics, 7, 2019-2027.
44. Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M. and Kreiman, G. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U.S.A., 101, 6062-6067.
45. Barabasi, A.L., Gulbahce, N. and Loscalzo, J. (2011) Network medicine: a network-based approach to human disease. Nat. Rev. Genet., 12, 56-68.
46. Gustafsson, M., Nestor, C.E., Zhang, H., Barabasi, A.L., Baranzini, S., Brunak, S., Chung, K.F., Federoff, H.J., Gavin, A.C., Meehan, R.R. et al. (2014) Modules, networks and systems medicine for understanding disease and aiding diagnosis. Genome Med., 6, 82.
47. GTEx Consortium. (2013) The Genotype-Tissue Expression (GTEx) project. Nat. Genet., 45, 580-585.
48. Wilhelm, M., Schlegl, J., Hahne, H., Moghaddas Gholami, A., Lieberenz, M., Savitski, M.M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H. et al. (2014) Mass-spectrometry-based draft of the human proteome. Nature, 509, 582-587.
49. Kim, M.S., Pinto, S.M., Getnet, D., Nirujogi, R.S., Manda, S.S., Chaerkady, R., Madugundu, A.K., Kelkar, D.S., Isserlin, R., Jain, S. et al. (2014) A draft map of the human proteome. Nature, 509, 575-581.
50. Uhlen, M., Fagerberg, L., Hallstrom, B.M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, A., Kampf, C., Sjostedt, E., Asplund, A. et al. (2015) Proteomics. Tissue-based map of the human proteome. Science, 347, 1260419.